Bioinformatics and statistics for metabarcoding studies in environmental microbiology and ecology - joint with CUSO EE

9-10 December 2019

Course in collaboration with the CUSO Doctoral Program in Ecology & Evolution

Organiser: Dr. Guillaume Lentendu, University of Neuchâtel



This course aims to provide an overview of the main bioinformatic and statistic tools used to conduct biodiversity analyses based on environmental sequencing and to give a step by step practical guide to the most commonly used tools for metabarcoding data analyses.



During the last decade, environmental sequencing has become a standard tool to monitor biodiversity for both micro- and macro-organisms. Following the development of high-throughput sequencing, a myriad of tools have been developed to efficiently process the ever increasing amount of sequence data produced. Target amplification of environmental DNA, also known as metabarcoding, is the most common and up-to-date technique used to assess the diversity of target organisms in the environment and is applied to a wide range of organisms, from bacteria, fungi and protists, to plant and insects.

During the courses, the participants will learn how to use bash and R scripting language for efficient processing of meta barcoding and biodiversity datasets. No previous knowledge of bash is needed, but basic R knowledge is requested.

The course will be split in two days:

Day 1 – From raw reads to OTU table:
 09:00 – 11:00:  general introduction onto the applications of metabarcoding to scientific questions in ecology and to the main bioinformatics analyses techniques.
 11:00 – 11:20:  tea & coffee break
 11:20 – 13:00:  introduction to UNIX environment and bash scripting applied to large sequence file manipulation
 13:00 – 14:00:  lunch break
 14:00 – 16:30:  Illumina MiSeq raw reads quality trimming and pair-end merging – hands-on parallel computation
 16:30 – 16:50:  tea & coffee break
 16:50 – 18:00:  ASV/OTU clustering and taxonomic assignment

Day 2 – Alpha and Beta diversity:
 09:00 – 11:00:  introduction to the R software and to the vegan, dplyr and ggplot packages
 11:00 – 11:20:  tea & coffee break
 11:20 – 13:00:  alpha diversity: normalization, measure and statistical tests
 13:00 – 14:00:  lunch break
 14:00 – 16:30:  taxonomic composition: publication ready figures and statistical tests
 16:30 – 16:50:  tea & coffee break
 16:50 – 18:00:  beta diversity: testing effect of experimental factors and parameters on community composition
 18:00 – 18:15:  feedback and farewell

Requirements for attending the workshop and practical information

No previous knowledge of bash is needed, but basic R knowledge is requested. Ideally, a previous attendance of an introductory course to R is recommended. For information: An Introduction to R, 4-7 June 2019, University of Lausanne

The course will take place in a computer room of the University of Neuchâtel. The students will use the provided computers (one computer per student with every software needed for the course already installed) and example datasets to realize all the bioinformatic and statistic practical duties.

The participants could bring there own computer, but should have all software already installed (A list with links of sotware to be installed can be provided upon request). No support to installation and configuration of software on personal computers will be provided.

If a participant wants to analyze his/her own metabarcoding dataset, he/she should contact the course instructor beforehand.

General information

Dates: 9-10 December 2019

Schedule: 8.55-18.15

Venue:  University of Neuchâtel, Faculté des Sciences, Emile-Argand 11, UniMail, building B, room B316 (room Florapolis)

ECTS: 1.0 (Research tools)

Evaluation: Full attendance and active participation

Information: Please contact Dr. Guillaume Lentendu or the doctoral program coordinator Dr Sara Santi (administration)

Registration fee: free for the participants of the Interuniversity doctoral program in Organismal Biology (DPOB) and CUSO Ecology & Evolution. Other or external participants should contact the coordinator of the Organismal Biology doctoral program for more information about the participation fee.

Travel expenses: For participants of the Interuniversity doctoral program in organismal biology (DPOB): see reimbursement conditions. For participants of the CUSO doctoral program in Ecology and Evolution: see CUSO E&E web site

Make sure to sign the attendance sheet each and every day and to take your certificate of attendance at the end of the course (no certificate will be sent by mail)


  • This course is free and open to all DPOB & CUSO EE PhD students (with registration priority until November 17)
  • Post-docs are welcome as long as places are available - a participation fee may be requested.
  • Maximum number of participants: 6 (DPOB) + 6 (CUSO EE) + 3 (other participants)

Registration through the web only: Closed. The course is fully booked.

Please note the cancellation policy (CHF 50).

Deadline: 24 November 2019